Nr1h4 (nuclear receptor subfamily 1 group H member 4) - Rat Genome Database

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Gene: Nr1h4 (nuclear receptor subfamily 1 group H member 4) Ictidomys tridecemlineatus
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Symbol: Nr1h4
Name: nuclear receptor subfamily 1 group H member 4
RGD ID: 12667464
Description: ENCODES a protein that exhibits bile acid binding (ortholog); DNA binding (ortholog); double-stranded DNA binding (ortholog); INVOLVED IN bile acid and bile salt transport (ortholog); bile acid metabolic process (ortholog); bile acid signaling pathway (ortholog); PARTICIPATES IN bile acid signaling pathway; ASSOCIATED WITH alcoholic hepatitis (ortholog); Animal Disease Models (ortholog); atherosclerosis (ortholog); FOUND IN nucleus (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: bile acid receptor; nuclear receptor subfamily 1 group H member 4, transcript variant X1; nuclear receptor subfamily 1 group H member 4, transcript variant X2
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: SpeTri2.0 - Squirrel SpeTri2.0 Assembly
Position:
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494520,304,852 - 20,379,409 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493649213,315,265 - 13,365,186 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
bile acid and bile salt transport  (ISO)
bile acid metabolic process  (IEA,ISO)
bile acid signaling pathway  (IEA,ISO)
cell-cell junction assembly  (IEA)
cellular glucose homeostasis  (IEA)
cellular response to bile acid  (IEA)
cellular response to fatty acid  (IEA)
cellular response to lipopolysaccharide  (IEA)
cellular response to organonitrogen compound  (IEA)
cellular response to xenobiotic stimulus  (ISO)
cellular triglyceride homeostasis  (IEA)
cholesterol homeostasis  (IEA,ISO)
defense response to bacterium  (IEA)
digestive tract development  (ISO)
DNA-templated transcription  (IEA,ISO)
fatty acid homeostasis  (IEA)
glucose homeostasis  (IEA,ISO)
hepatocyte proliferation  (ISO)
histone H3-R17 methylation  (ISO)
intracellular bile acid receptor signaling pathway  (IEA)
intracellular receptor signaling pathway  (IEA,ISO)
leukocyte migration involved in inflammatory response  (ISO)
lipid localization  (ISO)
liver regeneration  (ISO)
negative regulation of apoptotic process  (IEA)
negative regulation of collagen biosynthetic process  (ISO)
negative regulation of I-kappaB kinase/NF-kappaB signaling  (IEA)
negative regulation of inflammatory response  (IEA)
negative regulation of interleukin-1 production  (IEA)
negative regulation of interleukin-2 production  (IEA)
negative regulation of interleukin-6 production  (IEA)
negative regulation of monocyte chemotactic protein-1 production  (IEA)
negative regulation of NF-kappaB transcription factor activity  (IEA)
negative regulation of transcription by RNA polymerase II  (IEA,ISO)
negative regulation of triglyceride biosynthetic process  (ISO)
negative regulation of tumor necrosis factor production  (IEA)
negative regulation of tumor necrosis factor-mediated signaling pathway  (IEA)
negative regulation of type II interferon production  (IEA)
negative regulation of very-low-density lipoprotein particle remodeling  (IEA,ISO)
Notch signaling pathway  (IEA,ISO)
positive regulation of adipose tissue development  (IEA)
positive regulation of ammonia assimilation cycle  (IEA)
positive regulation of DNA-templated transcription  (IEA,ISO)
positive regulation of gene expression  (ISO)
positive regulation of glutamate metabolic process  (IEA)
positive regulation of insulin receptor signaling pathway  (IEA)
positive regulation of insulin secretion involved in cellular response to glucose stimulus  (IEA)
positive regulation of interleukin-17 production  (IEA)
positive regulation of phosphatidic acid biosynthetic process  (IEA)
positive regulation of transcription by RNA polymerase II  (IEA,ISO)
regulation of bile acid secretion  (ISO)
regulation of carbohydrate metabolic process  (ISO)
regulation of DNA-templated transcription  (IEA)
regulation of gene expression  (ISO)
regulation of insulin secretion involved in cellular response to glucose stimulus  (IEA)
regulation of lipid storage  (ISO)
regulation of low-density lipoprotein particle clearance  (IEA)
regulation of transcription by RNA polymerase II  (IEA,ISO)
regulation of urea metabolic process  (IEA)
response to 17alpha-ethynylestradiol  (ISO)
response to cholesterol  (ISO)
response to ethanol  (ISO)
response to fenofibrate  (ISO)
response to glucose  (ISO)
response to lipopolysaccharide  (ISO)
response to norepinephrine  (ISO)
response to nutrient levels  (ISO)
response to organic cyclic compound  (ISO)
response to xenobiotic stimulus  (ISO)
toll-like receptor 4 signaling pathway  (IEA)
toll-like receptor 9 signaling pathway  (IEA)
transcription by RNA polymerase II  (IEA,ISO)
triglyceride homeostasis  (IEA,ISO)

Cellular Component
euchromatin  (IEA)
nucleus  (IEA,ISO)
receptor complex  (IEA)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Genomics

Comparative Map Data
Nr1h4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494520,304,852 - 20,379,409 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493649213,315,265 - 13,365,186 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NR1H4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3812100,473,866 - 100,564,414 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl12100,473,708 - 100,564,414 (+)EnsemblGRCh38hg38GRCh38
GRCh3712100,867,644 - 100,958,192 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361299,391,810 - 99,481,774 (+)NCBINCBI36Build 36hg18NCBI36
Build 341299,370,146 - 99,460,111NCBI
Celera12100,532,992 - 100,622,995 (+)NCBICelera
Cytogenetic Map12q23.1NCBI
HuRef1297,928,334 - 98,018,410 (+)NCBIHuRef
CHM1_112100,833,597 - 100,923,679 (+)NCBICHM1_1
T2T-CHM13v2.012100,435,311 - 100,525,835 (+)NCBIT2T-CHM13v2.0
Nr1h4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391089,290,096 - 89,369,484 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1089,290,096 - 89,369,447 (-)EnsemblGRCm39 Ensembl
GRCm381089,454,234 - 89,533,645 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1089,454,234 - 89,533,585 (-)EnsemblGRCm38mm10GRCm38
MGSCv371088,916,979 - 88,996,367 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361088,884,177 - 88,936,426 (-)NCBIMGSCv36mm8
Celera1091,441,224 - 91,574,747 (-)NCBICelera
Cytogenetic Map10C2NCBI
cM Map1044.98NCBI
Nr1h4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2723,846,122 - 23,942,085 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl723,846,122 - 23,942,047 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx725,840,659 - 25,936,578 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0728,003,082 - 28,099,010 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0727,780,396 - 27,876,311 (-)NCBIRnor_WKY
Rnor_6.0730,003,429 - 30,162,095 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl730,003,429 - 30,162,056 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0730,170,397 - 30,214,796 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.0730,104,960 - 30,107,142 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4726,189,759 - 26,307,061 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1726,210,029 - 26,327,332 (-)NCBI
Celera720,992,814 - 21,085,820 (-)NCBICelera
Cytogenetic Map7q13NCBI
Nr1h4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540536,160,049 - 36,237,751 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540536,160,360 - 36,236,258 (+)NCBIChiLan1.0ChiLan1.0
NR1H4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.112101,457,885 - 101,548,058 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl12101,457,885 - 101,548,058 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01298,052,778 - 98,144,085 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
NR1H4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11539,497,313 - 39,608,120 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1539,536,290 - 39,608,116 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1539,876,387 - 39,987,365 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01540,161,103 - 40,272,109 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1540,200,071 - 40,271,741 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11539,418,531 - 39,529,420 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01539,525,061 - 39,636,033 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01539,799,183 - 39,910,169 (+)NCBIUU_Cfam_GSD_1.0
NR1H4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl583,604,294 - 83,684,604 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1583,607,222 - 83,732,668 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2587,754,914 - 87,828,507 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NR1H4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11195,792,428 - 95,877,989 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1195,792,996 - 95,878,293 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037149,156,310 - 149,247,016 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Nr1h4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247507,219,251 - 7,303,834 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247507,222,306 - 7,303,809 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Expression


Sequence


Reference Sequences
RefSeq Acc Id: XM_005322371   ⟹   XP_005322428
RefSeq Status:
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494520,304,852 - 20,354,772 (-)NCBI
SpeTri2.0NW_00493649213,315,265 - 13,365,186 (-)NCBI
Sequence:
RefSeq Acc Id: XM_005322372   ⟹   XP_005322429
RefSeq Status:
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494520,304,852 - 20,354,772 (-)NCBI
SpeTri2.0NW_00493649213,315,265 - 13,365,186 (-)NCBI
Sequence:
RefSeq Acc Id: XM_040279458   ⟹   XP_040135392
RefSeq Status:
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494520,304,852 - 20,379,174 (-)NCBI
RefSeq Acc Id: XM_040279464   ⟹   XP_040135398
RefSeq Status:
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494520,304,852 - 20,379,409 (-)NCBI
RefSeq Acc Id: XM_040279472   ⟹   XP_040135406
RefSeq Status:
Type: CODING
Position:
Squirrel AssemblyChrPosition (strand)Source
HiC_Itri_2NW_02440494520,304,852 - 20,379,173 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_005322429   ⟸   XM_005322372
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_005322428   ⟸   XM_005322371
- Peptide Label: isoform X1
- UniProtKB: I3MHY8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_040135398   ⟸   XM_040279464
- Peptide Label: isoform X3
- UniProtKB: A0A287DE48 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_040135392   ⟸   XM_040279458
- Peptide Label: isoform X3
- UniProtKB: A0A287DE48 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_040135406   ⟸   XM_040279472
- Peptide Label: isoform X4
Protein Domains
NR LBD   Nuclear receptor


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSTOG00000011771 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSSTOP00000010560 ENTREZGENE
  ENSSTOP00000010560.3 UniProtKB/TrEMBL
  ENSSTOP00000031809.1 UniProtKB/TrEMBL
Ensembl Transcript ENSSTOT00000011771.3 UniProtKB/TrEMBL
  ENSSTOT00000039771.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.565.10 UniProtKB/TrEMBL
  3.30.50.10 UniProtKB/TrEMBL
InterPro NHR-like_dom_sf UniProtKB/TrEMBL
  NR_LBD_NR1H4 UniProtKB/TrEMBL
  Nucl_hrmn_rcpt_lig-bd UniProtKB/TrEMBL
  Nuclear_hrmn_rcpt UniProtKB/TrEMBL
  ThyrH_rcpt UniProtKB/TrEMBL
  Znf_hrmn_rcpt UniProtKB/TrEMBL
  Znf_NHR/GATA UniProtKB/TrEMBL
NCBI Gene Nr1h4 ENTREZGENE
Pfam Hormone_recep UniProtKB/TrEMBL
  zf-C4 UniProtKB/TrEMBL
PRINTS STRDHORMONER UniProtKB/TrEMBL
  STROIDFINGER UniProtKB/TrEMBL
  THYROIDHORMR UniProtKB/TrEMBL
PROSITE NR_LBD UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_1 UniProtKB/TrEMBL
  NUCLEAR_REC_DBD_2 UniProtKB/TrEMBL
SMART HOLI UniProtKB/TrEMBL
  ZnF_C4 UniProtKB/TrEMBL
Superfamily-SCOP SSF48508 UniProtKB/TrEMBL
UniProt A0A287DE48 ENTREZGENE, UniProtKB/TrEMBL
  I3MHY8 ENTREZGENE, UniProtKB/TrEMBL